rs12580100

Variant names:

• chr12-56045425-A-G
• rs12580100

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.145 in 152,086 control chromosomes in the GnomAD database, including 1,869 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.15 (1869 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.431
• Publications: 44 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22072 AN: 151966 Hom.: 1867 Cov.: 31

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.117

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.143

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.145 AC: 22089 AN: 152086 Hom.: 1869 Cov.: 31 AF XY: 0.151 AC XY: 11210 AN XY: 74344

African (AFR) AF: 0.113 AC: 4670 AN: 41488

American (AMR) AF: 0.199 AC: 3042 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.117 AC: 407 AN: 3472

East Asian (EAS) AF: 0.229 AC: 1181 AN: 5162

South Asian (SAS) AF: 0.336 AC: 1616 AN: 4806

European-Finnish (FIN) AF: 0.155 AC: 1638 AN: 10594

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9065 AN: 67976

Other (OTH) AF: 0.148 AC: 313 AN: 2114

Alfa AF: 0.139 Hom.: 6900

Bravo AF: 0.142

Asia WGS AF: 0.310 AC: 1077 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.39
PhyloP100		0.43

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs12580100; hg19: chr12-56439209;